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--- lecture_notes:04-30-2010 [2010/05/02 22:05]
jstjohn
+++ lecture_notes:04-30-2010 [2010/05/05 20:53]
jmagasin
@@ Line 303: / Line 303: @@
 Even just getting the right answer within a factor of 10 was
 encouraging.
+===== Second set of lecture notes =====
+From Jonathan Magasin.
+Today's lecture covered files generated by Kevin's map-colorspace5
+script which will be necessary for the homework assignment: ordering
+the POG contigs.  Also covered: How to roughly estimate banana slug
+genome size.
+==== Homework assignment: assemble POG ====
+From the newer newbler we have a different set of contigs, thirty-one
+of them.  We also have mate pairs from SOLiD mapped to newbler
+assembly 5.  The assignment is to order and orient them the contigs.
+Kevin has posted his solution in the assembly directory
+(assemblies/Pog/map-colorspace5).
+=== 'delete' and 'invert' files ===
+The trim9 files are output from Kevin's map-colorspace5 script.  Most
+of them are not for us.  The 'delete' files are for mate pairs where
+both mapped but not at the appropriate distance: closer than 350
+bases, or more than 5000 bases apart.  These files can be studied to
+find massive deletions.
+'invert' files are for mate pairs that were on opposite strands (at
+any distance) and are useful for studying inversions.  However
+inversions are not so useful because they will not be within a single
+contig.
+The 'between contigs' files are for when the reads mapped to different
+contigs.  Only cases with unique mappings are in these files.  fixme:
+What file(s) is this?
+=== trim9.out ===
+The trim9.out file is a summary of what happened during mapping.
+Kmers are colorspace kmers.  These kmers are the lengths after
+trimming off nine.  'uniquly mapped' means one for the R3 and one for
+the F3.  Note that some of the summary stats are bugs (the 'wrong
+range' line) that have since been fixed.  [Kevin reran the script of
+Friday.]
+Compared to earlier mapping, Kevin has increased the agressiveness.
+The deletions ('wrong range' line) appear to be from reads taken from
+clones with multiple adapters.
+Strand biases (algorithmic) were checked for in the forward and
+backward counts of mapped reads.
+Tonight Kevin [reran] the mapping script.  The new output will
+include error rates by position. Sol requested these be called
+mismatches rather than errors.  Kevin said they are estimates of
+sequencing error.  They are in colorspace, and exclude indels.  In
+reality they are differences between the reads and assemblies, not
+errors.  But for all practical purposes when there is a mismatch
+between a read and the assembly the error is in the read.)
+=== trim9.joins ===
+The data we'll use is not in trim9.out, rather it is in trim9.joins.
+trim9.joins is computed from trim9-cross.rdb (which has reads that
+crossed a contig boundary).
+Looking at the first line: How many reads support contig 22 following
+contig 3?  34K.  The contigs lengths are there to see if a contig is
+short enough that mate pairs might span them.  E.g. what orderings are
+consistent with the listed contig orders: 2->3->4, or maybe 3 is very
+short so we have a mate pair that jumps over 3.
+A minus sign appearing before a contig name means to take the
+reverse-complement of that contig.  (And contig3 followed by contig22
+is the same as -contig22 followed by -contig3.)
+The last number on each line indicates if the mate pair were the
+optimal length (optimal is the peak of length distribution).  That
+number is the expected length of the gap between the contigs.  It is
+very rough.
+The file is sorted most-counts to fewest.  The stuff at bottom of the
+file is noise.  Only about first fifty lines are helpful.
+Long mate pairs are very helpful for disambiguating, and wish we had
+them for H.pylori.
+=== Your task ===
+Take the trim9.joins file and try to order and orient the contigs,
+knowing that some of them are duplicated, and that there is a virus in
+the mix and there should be one large chromosome.

Banana Slug Genomics

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